There are several communities developing software for the ArduPilot Mega platform. Currently, the communities supporting ArduPilot Mega are ArduCopter, ArduPirates and AeroQuad.
The Arducopter and ArduPirates share the same code base. The ArduPirates community has branched off and is developing the ArduCopter software for their own needs. I initially chose ArduPirates but recently switched to the ArduCopter code because the code is well commented, simpler and easier to understand. Both code bases work well, but I find Arducopter code easier to modify.
The only reason why I did not chose AeroQuad is because I could not get wireless communication with Scout working as I could with both ArduPirates and ArduCopter.
Wireless communication allows the freedom for on-the-fly tuning and reading sensor data from Scout without having to connect a USB cable to it. If I had GPS installed, wireless communication would also allow for real-time updating of the flight path without having to bring Scout back to the base station for programming.